It makes sense. I am not sure that I follow how you calculated the critical box size depending on the the concentration.
On Tue, Nov 14, 2017 at 9:12 AM, Alex <nedoma...@gmail.com> wrote: > It makes no difference whether you use -np/-nn or -conc. Your box is > simply too small to result in a nonzero ion count with something like 0.002 > M. The check is rather simple: a cubic box has to be larger than > (1/n)^(1/3). For 0.002 M, that critical box size is 9.4 nm. > > You can of course force any number of ions in there, but back-calculate > the corresponding concentration, given the box volume, and you'll see that > it's not what you want. This is exactly what GMX does when you call -conc. > > Alex > > > > On 11/13/2017 11:54 PM, Netaly Khazanov wrote: > >> Thanks for your prompt replay. >> I thougnt it would be more elegant way to do it using the commands. >> If not that is what I am going to do. >> Best, >> Netaly >> >> On Mon, Nov 13, 2017 at 2:37 PM, Hermann, Johannes < >> j.herm...@lrz.tu-muenchen.de> wrote: >> >> Hi Netaly, >>> >>> one way would be to calculate the number of Na, Cl, and Mg ions by hand, >>> i.e. with the box size and the respective concentrations, and add the >>> correct amount of ions in two steps, with the flags -np or -nn. E.g. in >>> the >>> first step you add Na and Cl and in the second you add Mg. >>> >>> All the best >>> >>> Johannes >>> >>> >>> On 13.11.2017 13:31, Netaly Khazanov wrote: >>> >>> Dear Gromacs User, >>>> >>>> Is it possible to simulate system with two salt concentrations , e.g. >>>> NaCl >>>> 0.1 mol/L and MgCl2 0.002 mol/liter? >>>> >>>> The commands that i am using you can see below: >>>> >>>> grompp_d -f ions.mdp -c ligand_MG_box_water.gro -p topol.top -o ions.tpr >>>> genion_d -s ions.tpr -o ligand_box_water_NaCL.gro -p topol.top -pname >>>> NA - >>>> nname CL -neutral -conc 0.1 >>>> grompp_d -f ions.mdp -c ligand_box_water_NACL.gro -p topol.top -o >>>> ions.tpr >>>> genion_d -s ions.tpr -o ligand_box_water_NaCL_MgCl2.gro -p topol.top >>>> -pname >>>> MG -pq 2 -nname CL -neutral -conc 0.002 >>>> >>>> The message that I got after the execution of the last command is :"No >>>> ions >>>> to add and no potential to calculate." >>>> >>>> Is it right way to do it? >>>> Thank you in advance. >>>> Netaly >>>> >>>> >>>> >>>> -- >>> ______________________________________ >>> *Technische Universität München* >>> *Johannes Hermann, M.Sc.* >>> Lehrstuhl für Bioverf >>> <https://maps.google.com/?q=uhl+f%C3%BCr+Bioverf&entry=gmail&source=g> >>> ahrenstechnik >>> Boltzmannstr. 15 >>> D-85748 Garching >>> Tel: +49 8928915730 >>> Fax: +49 8928915714 >>> >>> Email: j.herm...@lrz.tum.de >>> http://www.biovt.mw.tum.de/ >>> >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at http://www.gromacs.org/Support >>> /Mailing_Lists/GMX-Users_List before posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-requ...@gromacs.org. >>> >> >> >> >> > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Netaly -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.